| 2dba0a46 |
<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<meta name="author" content="Guangchuang Yu">
<link rel="canonical" href="https://guangchuangyu.github.io/ggtree/documentation/">
<link rel="shortcut icon" href="../img/favicon.ico">
<title>Documentation - ggtree</title>
<link href="../css/bootstrap-custom.min.css" rel="stylesheet">
<link href="../css/font-awesome-4.0.3.css" rel="stylesheet">
<link rel="stylesheet" href="../css/highlight.css">
<link href="../css/base.css" rel="stylesheet">
<!-- HTML5 shim and Respond.js IE8 support of HTML5 elements and media queries -->
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/libs/html5shiv/3.7.0/html5shiv.js"></script>
<script src="https://oss.maxcdn.com/libs/respond.js/1.3.0/respond.min.js"></script>
<![endif]-->
<script>
(function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){
(i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),
m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m)
})(window,document,'script','//www.google-analytics.com/analytics.js','ga');
ga('create', 'UA-77901140-1', 'guangchuangyu.github.io');
ga('send', 'pageview');
</script>
</head>
<body>
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<!-- Collapsed navigation -->
<div class="navbar-header">
<!-- Expander button -->
<button type="button" class="navbar-toggle" data-toggle="collapse" data-target=".navbar-collapse">
<span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<!-- Main title -->
<a class="navbar-brand" href="..">ggtree</a>
</div>
<!-- Expanded navigation -->
<div class="navbar-collapse collapse">
<!-- Main navigation -->
<ul class="nav navbar-nav">
<li >
<a href="..">Home</a>
</li>
<li class="active">
<a href="./">Documentation</a>
</li>
<li >
<a href="../faq/">FAQ</a>
</li>
<li >
<a href="../featuredArticles/">Featured Articles</a>
</li>
|
| 6949e7b6 |
<li >
<a href="../gallery/">Gallery</a>
</li>
|
| 2dba0a46 |
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown">My Software <b class="caret"></b></a>
<ul class="dropdown-menu">
<li >
<a href="../ChIPseeker/">ChIPseeker</a>
</li>
<li >
<a href="../clusterProfiler/">clusterProfiler</a>
</li>
<li >
<a href="../DOSE/">DOSE</a>
</li>
|
| d941d2fd |
<li >
<a href="../emojifont/">emojifont</a>
</li>
|
| 2dba0a46 |
<li >
<a href="../ggtree/">ggtree</a>
</li>
<li >
<a href="../GOSemSim/">GOSemSim</a>
</li>
|
| cc7b21be |
<li >
<a href="../meshes/">meshes</a>
</li>
|
| 2dba0a46 |
<li >
<a href="../ReactomePA/">ReactomePA</a>
</li>
|
| 144ddd31 |
<li >
<a href="../treeio/">treeio</a>
</li>
|
| 2dba0a46 |
</ul>
</li>
</ul>
<!-- Search, Navigation and Repo links -->
<ul class="nav navbar-nav navbar-right">
<li>
<a href="#" data-toggle="modal" data-target="#mkdocs_search_modal">
<i class="fa fa-search"></i> Search
</a>
</li>
<li >
<a rel="next" href="..">
<i class="fa fa-arrow-left"></i> Previous
</a>
</li>
<li >
<a rel="prev" href="../faq/">
Next <i class="fa fa-arrow-right"></i>
</a>
</li>
<li>
<a href="https://github.com/GuangchuangYu/ggtree">
<i class="fa fa-github"></i>
GitHub
</a>
</li>
</ul>
</div>
</div>
</div>
<div class="container">
<div class="col-md-3"><div class="bs-sidebar hidden-print affix well" role="complementary">
<ul class="nav bs-sidenav">
<li class="main active"><a href="#vignettes"> Vignettes</a></li>
<li class="main "><a href="#blog-posts"> Blog posts</a></li>
<li><a href="#news-and-updates"> News and updates</a></li>
<li><a href="#data-manipulation"> Data manipulation</a></li>
<li><a href="#tree-visualization"> Tree visualization</a></li>
<li><a href="#tree-annotation"> Tree annotation</a></li>
<li><a href="#tree-manipulation"> Tree manipulation</a></li>
<li><a href="#application"> Application</a></li>
<li><a href="#funny-stuff"> Funny stuff</a></li>
<li><a href="#users-feedback"> User's feedback</a></li>
<li class="main "><a href="#slides"> Slides</a></li>
<li class="main "><a href="#video"> Video</a></li>
<li class="main "><a href="#workflow"> Workflow</a></li>
</ul>
</div></div>
<div class="col-md-9" role="main">
<!-- AddToAny BEGIN -->
<div class="a2a_kit a2a_kit_size_32 a2a_default_style">
|
| 975b531a |
|
| 2dba0a46 |
<a class="a2a_dd" href="//www.addtoany.com/share"></a>
|
| 975b531a |
<a class="a2a_button_facebook"></a> <a class="a2a_button_twitter"></a>
|
| 2dba0a46 |
<a class="a2a_button_google_plus"></a>
|
| 975b531a |
<a class="a2a_button_pinterest"></a> <a class="a2a_button_reddit"></a>
<a class="a2a_button_sina_weibo"></a> <a class="a2a_button_wechat"></a>
|
| 2dba0a46 |
<a class="a2a_button_douban"></a>
|
| 975b531a |
|
| 2dba0a46 |
</div>
<script async src="//static.addtoany.com/menu/page.js"></script>
<!-- AddToAny END -->
<p><link rel="stylesheet" href="https://guangchuangyu.github.io/css/font-awesome.min.css"></p>
<h2 id="vignettes"><i class="fa fa-book"></i> Vignettes</h2>
<ul>
<li><a href="https://bioconductor.org/packages/devel/bioc/vignettes/ggtree/inst/doc/ggtree.html">ggtree</a></li>
|
| 975b531a |
<li><a href="https://bioconductor.org/packages/devel/bioc/vignettes/ggtree/inst/doc/treeImport.html">Tree Data
Import</a></li>
<li><a href="https://bioconductor.org/packages/devel/bioc/vignettes/ggtree/inst/doc/treeVisualization.html">Tree
Visualization</a></li>
<li><a href="https://bioconductor.org/packages/devel/bioc/vignettes/ggtree/inst/doc/treeAnnotation.html">Tree
Annotation</a></li>
<li><a href="https://bioconductor.org/packages/devel/bioc/vignettes/ggtree/inst/doc/treeManipulation.html">Tree
Manipulation</a></li>
<li><a href="https://bioconductor.org/packages/devel/bioc/vignettes/ggtree/inst/doc/advanceTreeAnnotation.html">Advance Tree
Annotation</a></li>
<li><a href="https://bioconductor.org/packages/devel/bioc/vignettes/ggtree/inst/doc/ggtreeUtilities.html">ggtree
utilities</a></li>
|
| 2dba0a46 |
</ul>
<h2 id="blog-posts"><i class="fa fa-wordpress"></i> Blog posts</h2>
<h3 id="news-and-updates"><i class="fa fa-angle-double-right"></i> News and updates</h3>
<ul>
|
| 975b531a |
<li><a href="https://guangchuangyu.github.io/2014/12/viewing-and-annotating-phylogenetic-tree-with-ggtree">viewing and annotating phylogenetic tree with
ggtree</a></li>
<li><a href="https://guangchuangyu.github.io/2015/01/ggtree-in-bioconductor-3.1">ggtree in Bioconductor
3.1</a></li>
<li><a href="https://guangchuangyu.github.io/2015/04/bioc-31-news-of-my-bioc-packages">BioC 3.1: NEWS of my BioC
packages</a></li>
<li><a href="https://guangchuangyu.github.io/2015/10/bioc-32-news-of-my-bioc-packages">BioC 3.2: NEWS of my BioC
packages</a></li>
<li><a href="https://guangchuangyu.github.io/2015/12/news-of-ggtree">News of
ggtree</a></li>
<li><a href="https://guangchuangyu.github.io/2016/05/bioc-33-news-of-my-bioc-packages/">BioC 3.3: NEWS of my BioC
packages</a></li>
<li><a href="https://guangchuangyu.github.io/2016/10/bioc-34-news-of-my-bioc-packages">BioC 3.4: NEWS of my BioC
packages</a></li>
<li><a href="https://guangchuangyu.github.io/2016/08/ggtree-paper-published">ggtree paper
published</a></li>
|
| 2dba0a46 |
</ul>
<h3 id="data-manipulation"><i class="fa fa-angle-double-right"></i> Data manipulation</h3>
<ul>
|
| 975b531a |
<li><a href="https://guangchuangyu.github.io/2015/09/subsetting-data-in-ggtree">subsetting data in
ggtree</a></li>
<li><a href="https://guangchuangyu.github.io/2016/01/ggtree-supports-phylip-tree-format">ggtree supports phylip tree
format</a></li>
<li><a href="http://guangchuangyu.github.io/2017/01/convert-graphic-object-to-tree-object-using-treeio/">convert graphic object to tree object using
treeio</a></li>
|
| 2dba0a46 |
</ul>
<h3 id="tree-visualization"><i class="fa fa-angle-double-right"></i> Tree visualization</h3>
<ul>
|
| 975b531a |
<li><a href="https://guangchuangyu.github.io/2015/02/ggtree---updating-a-tree-view/">ggtree - updating a tree
view</a></li>
<li><a href="https://guangchuangyu.github.io/2015/04/an-example-of-drawing-beast-tree-using-ggtree">an example of drawing beast tree using
ggtree</a></li>
<li><a href="http://www.molecularecologist.com/2017/02/phylogenetic-trees-in-r-using-ggtree/">Phylogenetic trees in R using
ggtree</a>
<i class="fa fa-arrow-left"></i> The Molecular Ecologist</li>
|
| 2dba0a46 |
</ul>
<h3 id="tree-annotation"><i class="fa fa-angle-double-right"></i> Tree annotation</h3>
<ul>
|
| 975b531a |
<li><a href="https://guangchuangyu.github.io/2016/01/label-edge-number-in-ggtree">label edge number in
ggtree</a></li>
<li><a href="http://guangchuangyu.github.io/2016/12/edge-coloring-with-user-data/">Edge coloring with user
data</a></li>
|
| 2dba0a46 |
<li><a href="https://guangchuangyu.github.io/2015/08/subview">subview</a></li>
|
| 975b531a |
<li><a href="https://guangchuangyu.github.io/2016/01/annotate-a-phylogenetic-tree-with-insets">Annotate a phylogenetic tree with
insets</a></li>
<li><a href="https://guangchuangyu.github.io/2015/08/ggtree-annotate-phylogenetic-tree-with-local-images">ggtree annotate phylogenetic tree with local
images</a></li>
<li><a href="https://guangchuangyu.github.io/2016/03/embed-images-in-ggplot2-via-subview-and-annotate-a-phylogenetic-tree-with-images-using-inset-function">embed images in ggplot2 via subview and annotate a phylogenetic
tree with images using inset
function</a></li>
<li><a href="https://guangchuangyu.github.io/2016/06/identify-method-for-ggtree">identify method for
ggtree</a></li>
<li><a href="https://guangchuangyu.github.io/2016/10/facet_plot-a-general-solution-to-associate-data-with-phylogenetic-tree/">facet_plot: a general solution to associate data with phylogenetic
tree</a></li>
<li><a href="https://guangchuangyu.github.io/2016/11/align-genomic-features-with-phylogenetic-tree/">align genomic features with phylogenetic
tree</a></li>
<li><a href="https://guangchuangyu.github.io/2016/10/xlim_tree-set-x-axis-limits-for-only-tree-panel/">xlim_tree: set x axis limits for only Tree
panel</a></li>
<li><a href="https://guangchuangyu.github.io/2016/12/add-layer-to-specific-panel-of-facet_plot-output/">add layer to specific panel of facet_plot
output</a></li>
|
| 2dba0a46 |
</ul>
<h3 id="tree-manipulation"><i class="fa fa-angle-double-right"></i> Tree manipulation</h3>
<ul>
|
| 975b531a |
<li><a href="https://guangchuangyu.github.io/2015/07/flip-and-rotate-branches-in-ggtree">flip and rotate branches in
ggtree</a></li>
|
| 2dba0a46 |
</ul>
<h3 id="application"><i class="fa fa-angle-double-right"></i> Application</h3>
<ul>
|
| 975b531a |
<li><a href="https://guangchuangyu.github.io/2016/09/ggtree-for-microbiome-data/">ggtree for microbiome
data</a></li>
<li><a href="https://guangchuangyu.github.io/2016/09/ggtree-for-outbreak-data/">ggtree for outbreak
data</a></li>
<li><a href="http://guangchuangyu.github.io/2016/12/ggtree-version-of-plottree/">ggtree version of
plotTree</a></li>
<li><a href="https://guangchuangyu.github.io/2016/10/reproducible-logo-generated-by-ggtree">reproducible logo generated by
ggtree</a></li>
|
| 2dba0a46 |
</ul>
<h3 id="funny-stuff"><i class="fa fa-angle-double-right"></i> Funny stuff</h3>
<ul>
|
| 975b531a |
<li><a href="https://guangchuangyu.github.io/2015/06/ggtree-with-funny-fonts">ggtree with funny
fonts</a></li>
<li><a href="https://guangchuangyu.github.io/2015/09/comic-phylogenetic-tree-with-ggtree-and-comicr">comic phylogenetic tree with ggtree and
comicR</a></li>
<li><a href="https://guangchuangyu.github.io/2015/12/use-emoji-font-in-r">use emoji font in
R</a></li>
|
| 2dba0a46 |
</ul>
<h3 id="users-feedback"><i class="fa fa-angle-double-right"></i> User's feedback</h3>
<ul>
|
| 975b531a |
<li><a href="https://guangchuangyu.github.io/2016/02/tweets-of-ggtree">tweets of
ggtree</a></li>
<li>Join the group chat on
<a href="https://twitter.com/hashtag/ggtree"><i class="fa fa-twitter fa-lg"></i></a>
and
<a href="http://huati.weibo.com/k/ggtree"><i class="fa fa-weibo fa-lg"></i></a></li>
|
| 2dba0a46 |
</ul>
|
| 975b531a |
<p><i class="fa fa-hand-o-right"></i> Find out more on
<a href="https://guangchuangyu.github.io/tags/ggtree/">https://guangchuangyu.github.io/tags/ggtree/</a>.</p>
|
| 2dba0a46 |
<h2 id="slides"><i class="fa fa-slideshare"></i> Slides</h2>
<ul>
|
| 975b531a |
<li><a href="https://guangchuangyu.github.io/presentation/2014-ggplot2/">Generating publication quality figures using R &
ggplot2</a></li>
<li><a href="https://guangchuangyu.github.io/presentation/2016-ggtree-chinar/">ggtree for visualization and annotation of phylogenetic
trees</a></li>
|
| 2dba0a46 |
</ul>
<h2 id="video"><i class="fa fa-youtube-play"></i> Video</h2>
<ul>
|
| 975b531a |
<li><a href="https://www.youtube.com/watch?v=KcF8Ec38mzI">interactive clade
highlighting</a></li>
<li><a href="https://www.youtube.com/watch?v=lKNn4QlPO0E">interactive rotating
clades</a></li>
<li><a href="https://www.youtube.com/watch?v=SmcceRD_jxg">interactive clade
labeling</a></li>
|
| 2dba0a46 |
</ul>
<h2 id="workflow"><i class="fa fa-gift"></i> Workflow</h2>
<ul>
|
| 975b531a |
<li><a href="https://rpubs.com/gutijosh9430/124817">recreate a tree from a publication (<strong>Bloom</strong> <em>et al</em>,
<strong><em>Science</em></strong> 2010)</a></li>
|
| 2dba0a46 |
</ul></div>
</div>
<footer class="col-md-12">
<hr>
<center>Copyright © 2016 <a href="https://guangchuangyu.github.io">Guangchuang Yu</a>.<div style="width:250px;margin:auto;"><script type="text/javascript" src="//rf.revolvermaps.com/0/0/7.js?i=5qpvv5zz7fp&m=0&c=ff0000&cr1=ffffff&sx=0" async="async"></script></div></center>
<center>Documentation built with <a href="http://www.mkdocs.org/">MkDocs</a>.</center>
</footer>
<script src="../js/jquery-1.10.2.min.js"></script>
<script src="../js/bootstrap-3.0.3.min.js"></script>
<script src="../js/highlight.pack.js"></script>
<script>var base_url = '..';</script>
<script data-main="../mkdocs/js/search.js" src="../mkdocs/js/require.js"></script>
<script src="../js/base.js"></script>
<div class="modal" id="mkdocs_search_modal" tabindex="-1" role="dialog" aria-labelledby="Search Modal" aria-hidden="true">
<div class="modal-dialog">
<div class="modal-content">
<div class="modal-header">
<button type="button" class="close" data-dismiss="modal"><span aria-hidden="true">×</span><span class="sr-only">Close</span></button>
<h4 class="modal-title" id="exampleModalLabel">Search</h4>
</div>
<div class="modal-body">
<p>
From here you can search these documents. Enter
your search terms below.
</p>
<form role="form">
<div class="form-group">
<input type="text" class="form-control" placeholder="Search..." id="mkdocs-search-query">
</div>
</form>
<div id="mkdocs-search-results"></div>
</div>
<div class="modal-footer">
</div>
</div>
</div>
</div>
</body>
</html>
|
